Starting phenix.real_space_refine on Sat Apr 26 15:02:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jgc_36230/04_2025/8jgc_36230.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jgc_36230/04_2025/8jgc_36230.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jgc_36230/04_2025/8jgc_36230.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jgc_36230/04_2025/8jgc_36230.map" model { file = "/net/cci-nas-00/data/ceres_data/8jgc_36230/04_2025/8jgc_36230.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jgc_36230/04_2025/8jgc_36230.cif" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 7 5.16 5 C 987 2.51 5 N 249 2.21 5 O 273 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 1516 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1516 Classifications: {'peptide': 202} Incomplete info: {'backbone_only': 2} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 191} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.43, per 1000 atoms: 2.92 Number of scatterers: 1516 At special positions: 0 Unit cell: (56.43, 51.3, 58.995, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 7 16.00 O 273 8.00 N 249 7.00 C 987 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 165 " - pdb=" SG CYS A 203 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.38 Conformation dependent library (CDL) restraints added in 187.8 milliseconds 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 362 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 2 sheets defined 45.5% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 Processing helix chain 'A' and resid 22 through 35 Processing helix chain 'A' and resid 47 through 62 removed outlier: 5.273A pdb=" N PHE A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N LEU A 58 " --> pdb=" O GLU A 54 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU A 60 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET A 61 " --> pdb=" O PHE A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 82 Processing helix chain 'A' and resid 93 through 104 Processing helix chain 'A' and resid 113 through 122 Processing helix chain 'A' and resid 185 through 203 removed outlier: 3.892A pdb=" N GLU A 191 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LYS A 194 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA A 195 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE A 196 " --> pdb=" O LYS A 192 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU A 198 " --> pdb=" O LYS A 194 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 16 removed outlier: 3.687A pdb=" N THR A 42 " --> pdb=" O LEU A 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 88 61 hydrogen bonds defined for protein. 183 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.36 Time building geometry restraints manager: 0.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 291 1.33 - 1.45: 328 1.45 - 1.57: 914 1.57 - 1.70: 0 1.70 - 1.82: 12 Bond restraints: 1545 Sorted by residual: bond pdb=" C VAL A 182 " pdb=" O VAL A 182 " ideal model delta sigma weight residual 1.236 1.209 0.027 1.19e-02 7.06e+03 5.33e+00 bond pdb=" C LEU A 128 " pdb=" O LEU A 128 " ideal model delta sigma weight residual 1.234 1.202 0.032 1.51e-02 4.39e+03 4.56e+00 bond pdb=" CA VAL A 15 " pdb=" C VAL A 15 " ideal model delta sigma weight residual 1.523 1.497 0.026 1.27e-02 6.20e+03 4.10e+00 bond pdb=" CA LEU A 16 " pdb=" C LEU A 16 " ideal model delta sigma weight residual 1.524 1.500 0.024 1.23e-02 6.61e+03 3.83e+00 bond pdb=" CA ILE A 127 " pdb=" CB ILE A 127 " ideal model delta sigma weight residual 1.537 1.513 0.024 1.26e-02 6.30e+03 3.61e+00 ... (remaining 1540 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 1962 2.12 - 4.24: 107 4.24 - 6.36: 12 6.36 - 8.48: 2 8.48 - 10.60: 1 Bond angle restraints: 2084 Sorted by residual: angle pdb=" N VAL A 182 " pdb=" CA VAL A 182 " pdb=" C VAL A 182 " ideal model delta sigma weight residual 109.34 119.94 -10.60 2.08e+00 2.31e-01 2.60e+01 angle pdb=" N ALA A 180 " pdb=" CA ALA A 180 " pdb=" C ALA A 180 " ideal model delta sigma weight residual 112.23 106.50 5.73 1.26e+00 6.30e-01 2.07e+01 angle pdb=" N SER A 179 " pdb=" CA SER A 179 " pdb=" C SER A 179 " ideal model delta sigma weight residual 110.80 118.97 -8.17 2.13e+00 2.20e-01 1.47e+01 angle pdb=" N LEU A 128 " pdb=" CA LEU A 128 " pdb=" C LEU A 128 " ideal model delta sigma weight residual 109.65 115.33 -5.68 1.56e+00 4.11e-01 1.33e+01 angle pdb=" N LEU A 16 " pdb=" CA LEU A 16 " pdb=" C LEU A 16 " ideal model delta sigma weight residual 108.73 114.18 -5.45 1.63e+00 3.76e-01 1.12e+01 ... (remaining 2079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.51: 826 15.51 - 31.03: 67 31.03 - 46.54: 24 46.54 - 62.05: 14 62.05 - 77.57: 1 Dihedral angle restraints: 932 sinusoidal: 368 harmonic: 564 Sorted by residual: dihedral pdb=" CB CYS A 165 " pdb=" SG CYS A 165 " pdb=" SG CYS A 203 " pdb=" CB CYS A 203 " ideal model delta sinusoidal sigma weight residual -86.00 -37.13 -48.87 1 1.00e+01 1.00e-02 3.29e+01 dihedral pdb=" CA VAL A 154 " pdb=" C VAL A 154 " pdb=" N PRO A 155 " pdb=" CA PRO A 155 " ideal model delta harmonic sigma weight residual -180.00 -161.75 -18.25 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA MET A 144 " pdb=" C MET A 144 " pdb=" N LYS A 145 " pdb=" CA LYS A 145 " ideal model delta harmonic sigma weight residual 180.00 163.80 16.20 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 168 0.059 - 0.118: 54 0.118 - 0.177: 17 0.177 - 0.236: 3 0.236 - 0.295: 2 Chirality restraints: 244 Sorted by residual: chirality pdb=" CA SER A 179 " pdb=" N SER A 179 " pdb=" C SER A 179 " pdb=" CB SER A 179 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA THR A 126 " pdb=" N THR A 126 " pdb=" C THR A 126 " pdb=" CB THR A 126 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA VAL A 13 " pdb=" N VAL A 13 " pdb=" C VAL A 13 " pdb=" CB VAL A 13 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 241 not shown) Planarity restraints: 263 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 12 " 0.015 2.00e-02 2.50e+03 2.87e-02 8.24e+00 pdb=" C ILE A 12 " -0.050 2.00e-02 2.50e+03 pdb=" O ILE A 12 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL A 13 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 167 " 0.008 2.00e-02 2.50e+03 1.46e-02 5.36e+00 pdb=" CG TRP A 167 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP A 167 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP A 167 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 167 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 167 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 167 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 167 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 167 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 167 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 137 " -0.036 5.00e-02 4.00e+02 5.41e-02 4.68e+00 pdb=" N PRO A 138 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 138 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 138 " -0.030 5.00e-02 4.00e+02 ... (remaining 260 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 349 2.78 - 3.31: 1482 3.31 - 3.84: 2330 3.84 - 4.37: 2780 4.37 - 4.90: 4873 Nonbonded interactions: 11814 Sorted by model distance: nonbonded pdb=" N ILE A 65 " pdb=" OE2 GLU A 85 " model vdw 2.251 3.120 nonbonded pdb=" OG SER A 97 " pdb=" NE2 HIS A 125 " model vdw 2.274 3.120 nonbonded pdb=" OD1 ASN A 160 " pdb=" ND2 ASN A 163 " model vdw 2.298 3.120 nonbonded pdb=" CD1 LEU A 16 " pdb=" CG2 VAL A 182 " model vdw 2.306 3.880 nonbonded pdb=" OE2 GLU A 22 " pdb=" CD LYS A 26 " model vdw 2.501 3.440 ... (remaining 11809 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 12.570 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 1546 Z= 0.378 Angle : 1.045 10.602 2086 Z= 0.592 Chirality : 0.068 0.295 244 Planarity : 0.008 0.054 263 Dihedral : 15.174 77.566 567 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 23.58 Ramachandran Plot: Outliers : 1.00 % Allowed : 9.00 % Favored : 90.00 % Rotamer: Outliers : 4.35 % Allowed : 1.86 % Favored : 93.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.55), residues: 200 helix: -1.91 (0.47), residues: 97 sheet: -1.00 (1.21), residues: 23 loop : -3.06 (0.65), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.009 TRP A 167 HIS 0.004 0.001 HIS A 10 PHE 0.016 0.003 PHE A 86 TYR 0.006 0.003 TYR A 107 ARG 0.001 0.000 ARG A 201 Details of bonding type rmsd hydrogen bonds : bond 0.13558 ( 61) hydrogen bonds : angle 6.96054 ( 183) SS BOND : bond 0.00476 ( 1) SS BOND : angle 0.82821 ( 2) covalent geometry : bond 0.00796 ( 1545) covalent geometry : angle 1.04544 ( 2084) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.162 Fit side-chains REVERT: A 49 ASP cc_start: 0.7927 (p0) cc_final: 0.7647 (p0) REVERT: A 112 MET cc_start: 0.4726 (ttt) cc_final: 0.4401 (ttp) REVERT: A 191 GLU cc_start: 0.7528 (tm-30) cc_final: 0.7305 (tm-30) outliers start: 7 outliers final: 5 residues processed: 28 average time/residue: 0.1132 time to fit residues: 3.7630 Evaluate side-chains 27 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 179 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 0.2980 chunk 15 optimal weight: 0.9980 chunk 8 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 12 optimal weight: 0.2980 chunk 19 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.123119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.103742 restraints weight = 1892.758| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.35 r_work: 0.3282 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 1546 Z= 0.106 Angle : 0.537 3.704 2086 Z= 0.283 Chirality : 0.048 0.141 244 Planarity : 0.006 0.038 263 Dihedral : 8.291 57.255 215 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.73 % Allowed : 6.83 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.60), residues: 200 helix: -0.75 (0.51), residues: 91 sheet: -0.34 (1.12), residues: 27 loop : -1.92 (0.74), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 167 HIS 0.002 0.001 HIS A 10 PHE 0.018 0.001 PHE A 196 TYR 0.002 0.001 TYR A 107 ARG 0.001 0.000 ARG A 201 Details of bonding type rmsd hydrogen bonds : bond 0.03433 ( 61) hydrogen bonds : angle 4.83234 ( 183) SS BOND : bond 0.00182 ( 1) SS BOND : angle 1.19119 ( 2) covalent geometry : bond 0.00241 ( 1545) covalent geometry : angle 0.53562 ( 2084) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.186 Fit side-chains REVERT: A 49 ASP cc_start: 0.8371 (p0) cc_final: 0.8048 (p0) REVERT: A 112 MET cc_start: 0.4761 (ttt) cc_final: 0.4277 (ttp) REVERT: A 144 MET cc_start: 0.7776 (ttp) cc_final: 0.7378 (ttm) REVERT: A 191 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7802 (tm-30) outliers start: 6 outliers final: 3 residues processed: 33 average time/residue: 0.1359 time to fit residues: 5.2533 Evaluate side-chains 24 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 185 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 4 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 2 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.122854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.102989 restraints weight = 1899.706| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.36 r_work: 0.3276 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1546 Z= 0.108 Angle : 0.520 3.460 2086 Z= 0.273 Chirality : 0.049 0.146 244 Planarity : 0.005 0.036 263 Dihedral : 5.766 49.786 208 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.24 % Allowed : 13.66 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.61), residues: 200 helix: -0.48 (0.52), residues: 93 sheet: 0.63 (1.27), residues: 22 loop : -1.91 (0.73), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 167 HIS 0.003 0.001 HIS A 10 PHE 0.009 0.001 PHE A 57 TYR 0.003 0.001 TYR A 107 ARG 0.002 0.001 ARG A 17 Details of bonding type rmsd hydrogen bonds : bond 0.02939 ( 61) hydrogen bonds : angle 4.40615 ( 183) SS BOND : bond 0.00033 ( 1) SS BOND : angle 0.95138 ( 2) covalent geometry : bond 0.00257 ( 1545) covalent geometry : angle 0.51974 ( 2084) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.175 Fit side-chains REVERT: A 112 MET cc_start: 0.4882 (ttt) cc_final: 0.4482 (ttp) REVERT: A 144 MET cc_start: 0.7670 (ttp) cc_final: 0.7340 (ttm) REVERT: A 191 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7764 (tm-30) outliers start: 2 outliers final: 2 residues processed: 24 average time/residue: 0.1512 time to fit residues: 4.2136 Evaluate side-chains 22 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 185 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 3 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 9 optimal weight: 9.9990 chunk 1 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.120343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.100999 restraints weight = 1868.085| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.30 r_work: 0.3250 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 1546 Z= 0.147 Angle : 0.547 3.835 2086 Z= 0.286 Chirality : 0.050 0.144 244 Planarity : 0.005 0.037 263 Dihedral : 4.729 26.274 206 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.86 % Allowed : 13.66 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.61), residues: 200 helix: -0.31 (0.53), residues: 91 sheet: 0.49 (1.26), residues: 22 loop : -2.04 (0.70), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 167 HIS 0.003 0.001 HIS A 10 PHE 0.010 0.002 PHE A 86 TYR 0.005 0.002 TYR A 107 ARG 0.002 0.001 ARG A 17 Details of bonding type rmsd hydrogen bonds : bond 0.03353 ( 61) hydrogen bonds : angle 4.52142 ( 183) SS BOND : bond 0.00091 ( 1) SS BOND : angle 0.55292 ( 2) covalent geometry : bond 0.00369 ( 1545) covalent geometry : angle 0.54688 ( 2084) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.189 Fit side-chains REVERT: A 92 LEU cc_start: 0.8465 (mt) cc_final: 0.8225 (mm) REVERT: A 112 MET cc_start: 0.4992 (ttt) cc_final: 0.4580 (ttp) REVERT: A 144 MET cc_start: 0.7997 (ttp) cc_final: 0.7605 (ttm) REVERT: A 191 GLU cc_start: 0.8362 (tm-30) cc_final: 0.8075 (tm-30) outliers start: 3 outliers final: 3 residues processed: 26 average time/residue: 0.1500 time to fit residues: 4.5072 Evaluate side-chains 22 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 185 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 13 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.121891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.102136 restraints weight = 1899.405| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.34 r_work: 0.3264 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1546 Z= 0.113 Angle : 0.493 3.490 2086 Z= 0.258 Chirality : 0.048 0.136 244 Planarity : 0.005 0.036 263 Dihedral : 4.412 23.536 206 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.86 % Allowed : 16.77 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.61), residues: 200 helix: -0.18 (0.52), residues: 93 sheet: 0.72 (1.28), residues: 22 loop : -1.63 (0.72), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP A 167 HIS 0.003 0.001 HIS A 10 PHE 0.009 0.001 PHE A 57 TYR 0.004 0.001 TYR A 107 ARG 0.002 0.000 ARG A 17 Details of bonding type rmsd hydrogen bonds : bond 0.02949 ( 61) hydrogen bonds : angle 4.34699 ( 183) SS BOND : bond 0.00130 ( 1) SS BOND : angle 0.55241 ( 2) covalent geometry : bond 0.00276 ( 1545) covalent geometry : angle 0.49323 ( 2084) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.179 Fit side-chains REVERT: A 112 MET cc_start: 0.4749 (ttt) cc_final: 0.4337 (ttp) REVERT: A 144 MET cc_start: 0.7770 (ttp) cc_final: 0.7409 (ttm) REVERT: A 191 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7759 (tm-30) outliers start: 3 outliers final: 3 residues processed: 24 average time/residue: 0.1824 time to fit residues: 4.9844 Evaluate side-chains 21 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 18 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 185 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 1 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 14 optimal weight: 0.0470 chunk 12 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 0.2980 overall best weight: 1.1882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.122808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.102774 restraints weight = 1945.443| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.41 r_work: 0.3266 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1546 Z= 0.105 Angle : 0.473 3.486 2086 Z= 0.246 Chirality : 0.047 0.132 244 Planarity : 0.005 0.035 263 Dihedral : 4.156 18.992 206 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.86 % Allowed : 16.77 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.61), residues: 200 helix: 0.02 (0.53), residues: 93 sheet: 0.79 (1.29), residues: 22 loop : -1.37 (0.71), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 167 HIS 0.003 0.001 HIS A 10 PHE 0.008 0.001 PHE A 57 TYR 0.004 0.001 TYR A 107 ARG 0.001 0.000 ARG A 17 Details of bonding type rmsd hydrogen bonds : bond 0.02811 ( 61) hydrogen bonds : angle 4.26276 ( 183) SS BOND : bond 0.00274 ( 1) SS BOND : angle 0.61150 ( 2) covalent geometry : bond 0.00257 ( 1545) covalent geometry : angle 0.47259 ( 2084) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.190 Fit side-chains REVERT: A 92 LEU cc_start: 0.8440 (mt) cc_final: 0.8124 (mm) REVERT: A 112 MET cc_start: 0.4776 (ttt) cc_final: 0.4356 (ttp) REVERT: A 144 MET cc_start: 0.7768 (ttp) cc_final: 0.7439 (ttm) REVERT: A 191 GLU cc_start: 0.8004 (tm-30) cc_final: 0.7768 (tm-30) outliers start: 3 outliers final: 2 residues processed: 25 average time/residue: 0.1585 time to fit residues: 4.5983 Evaluate side-chains 21 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 19 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 185 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 11 optimal weight: 0.9990 chunk 5 optimal weight: 7.9990 chunk 8 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.120099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.101478 restraints weight = 2028.646| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.07 r_work: 0.3255 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1546 Z= 0.110 Angle : 0.499 5.285 2086 Z= 0.261 Chirality : 0.047 0.131 244 Planarity : 0.005 0.035 263 Dihedral : 3.919 12.812 205 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.24 % Allowed : 18.01 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.61), residues: 200 helix: 0.15 (0.53), residues: 93 sheet: 0.84 (1.31), residues: 22 loop : -1.24 (0.72), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 167 HIS 0.003 0.001 HIS A 10 PHE 0.008 0.001 PHE A 57 TYR 0.004 0.001 TYR A 107 ARG 0.001 0.000 ARG A 17 Details of bonding type rmsd hydrogen bonds : bond 0.02760 ( 61) hydrogen bonds : angle 4.27685 ( 183) SS BOND : bond 0.00245 ( 1) SS BOND : angle 0.48693 ( 2) covalent geometry : bond 0.00269 ( 1545) covalent geometry : angle 0.49866 ( 2084) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.168 Fit side-chains REVERT: A 92 LEU cc_start: 0.8390 (mt) cc_final: 0.8127 (mm) REVERT: A 112 MET cc_start: 0.4880 (ttt) cc_final: 0.4445 (ttp) REVERT: A 144 MET cc_start: 0.7746 (ttp) cc_final: 0.7393 (ttm) REVERT: A 191 GLU cc_start: 0.8381 (tm-30) cc_final: 0.8102 (tm-30) outliers start: 2 outliers final: 2 residues processed: 25 average time/residue: 0.1518 time to fit residues: 4.4014 Evaluate side-chains 22 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 185 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 8 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 14 optimal weight: 0.0370 chunk 9 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.118511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.099856 restraints weight = 2029.998| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.09 r_work: 0.3227 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1546 Z= 0.136 Angle : 0.523 4.776 2086 Z= 0.273 Chirality : 0.049 0.137 244 Planarity : 0.005 0.038 263 Dihedral : 4.146 14.393 205 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 1.24 % Allowed : 19.25 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.60), residues: 200 helix: -0.02 (0.51), residues: 94 sheet: 0.68 (1.30), residues: 22 loop : -1.28 (0.71), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 167 HIS 0.003 0.001 HIS A 10 PHE 0.010 0.002 PHE A 86 TYR 0.006 0.002 TYR A 107 ARG 0.003 0.001 ARG A 77 Details of bonding type rmsd hydrogen bonds : bond 0.03145 ( 61) hydrogen bonds : angle 4.47619 ( 183) SS BOND : bond 0.00247 ( 1) SS BOND : angle 0.42417 ( 2) covalent geometry : bond 0.00338 ( 1545) covalent geometry : angle 0.52342 ( 2084) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.178 Fit side-chains REVERT: A 92 LEU cc_start: 0.8385 (mt) cc_final: 0.8151 (mm) REVERT: A 112 MET cc_start: 0.5037 (ttt) cc_final: 0.4580 (ttp) REVERT: A 144 MET cc_start: 0.7898 (ttp) cc_final: 0.7528 (ttm) REVERT: A 191 GLU cc_start: 0.8382 (tm-30) cc_final: 0.8106 (tm-30) outliers start: 2 outliers final: 2 residues processed: 24 average time/residue: 0.1531 time to fit residues: 4.2612 Evaluate side-chains 22 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 185 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 14 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 6 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.118121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.099501 restraints weight = 2082.560| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.10 r_work: 0.3226 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1546 Z= 0.134 Angle : 0.515 4.371 2086 Z= 0.268 Chirality : 0.049 0.136 244 Planarity : 0.005 0.039 263 Dihedral : 4.134 14.192 205 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.24 % Allowed : 19.25 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.60), residues: 200 helix: 0.06 (0.51), residues: 94 sheet: 0.64 (1.29), residues: 22 loop : -1.21 (0.71), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 167 HIS 0.003 0.001 HIS A 10 PHE 0.010 0.002 PHE A 86 TYR 0.006 0.002 TYR A 107 ARG 0.005 0.001 ARG A 77 Details of bonding type rmsd hydrogen bonds : bond 0.03130 ( 61) hydrogen bonds : angle 4.50450 ( 183) SS BOND : bond 0.00248 ( 1) SS BOND : angle 0.41980 ( 2) covalent geometry : bond 0.00333 ( 1545) covalent geometry : angle 0.51501 ( 2084) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.186 Fit side-chains REVERT: A 92 LEU cc_start: 0.8371 (mt) cc_final: 0.8133 (mm) REVERT: A 112 MET cc_start: 0.4912 (ttt) cc_final: 0.4506 (ttp) REVERT: A 144 MET cc_start: 0.7958 (ttp) cc_final: 0.7611 (ttm) REVERT: A 191 GLU cc_start: 0.8375 (tm-30) cc_final: 0.8093 (tm-30) outliers start: 2 outliers final: 2 residues processed: 23 average time/residue: 0.1633 time to fit residues: 4.3699 Evaluate side-chains 23 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 185 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 7 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 0.0470 chunk 8 optimal weight: 4.9990 chunk 16 optimal weight: 0.2980 chunk 6 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 1 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.6282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.121710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.103461 restraints weight = 2004.772| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.01 r_work: 0.3292 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 1546 Z= 0.087 Angle : 0.446 4.511 2086 Z= 0.234 Chirality : 0.045 0.123 244 Planarity : 0.005 0.035 263 Dihedral : 3.738 12.095 205 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.62 % Allowed : 20.50 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.62), residues: 200 helix: 0.47 (0.52), residues: 94 sheet: 0.99 (1.30), residues: 22 loop : -0.92 (0.75), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 167 HIS 0.003 0.001 HIS A 10 PHE 0.008 0.001 PHE A 196 TYR 0.003 0.001 TYR A 107 ARG 0.001 0.000 ARG A 77 Details of bonding type rmsd hydrogen bonds : bond 0.02499 ( 61) hydrogen bonds : angle 4.23158 ( 183) SS BOND : bond 0.00070 ( 1) SS BOND : angle 0.45075 ( 2) covalent geometry : bond 0.00209 ( 1545) covalent geometry : angle 0.44643 ( 2084) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.171 Fit side-chains REVERT: A 92 LEU cc_start: 0.8338 (mt) cc_final: 0.8072 (mm) REVERT: A 112 MET cc_start: 0.4995 (ttt) cc_final: 0.4602 (ttp) REVERT: A 144 MET cc_start: 0.7680 (ttp) cc_final: 0.7397 (ttm) REVERT: A 191 GLU cc_start: 0.8396 (tm-30) cc_final: 0.8098 (tm-30) outliers start: 1 outliers final: 1 residues processed: 24 average time/residue: 0.1630 time to fit residues: 4.5255 Evaluate side-chains 23 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 7 optimal weight: 8.9990 chunk 4 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.121747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.103155 restraints weight = 2063.893| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.07 r_work: 0.3287 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 1546 Z= 0.092 Angle : 0.455 4.350 2086 Z= 0.236 Chirality : 0.046 0.123 244 Planarity : 0.005 0.035 263 Dihedral : 3.702 12.686 205 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.62 % Allowed : 21.12 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.62), residues: 200 helix: 0.61 (0.52), residues: 94 sheet: 1.06 (1.30), residues: 22 loop : -0.77 (0.75), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 167 HIS 0.002 0.001 HIS A 10 PHE 0.011 0.001 PHE A 99 TYR 0.003 0.001 TYR A 107 ARG 0.001 0.000 ARG A 17 Details of bonding type rmsd hydrogen bonds : bond 0.02608 ( 61) hydrogen bonds : angle 4.22479 ( 183) SS BOND : bond 0.00301 ( 1) SS BOND : angle 0.34024 ( 2) covalent geometry : bond 0.00221 ( 1545) covalent geometry : angle 0.45489 ( 2084) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1627.43 seconds wall clock time: 28 minutes 57.61 seconds (1737.61 seconds total)